The rMBP dropped the infrared receiver making Apple Remote useless with it. It's a shame, since Airplay + Apple TV + Apple Remote would have worked as a perfect combo.

So, while playing a movie with Quicktime / VLC and streaming it to the TV, how can I control the playing (pause, skip, rewind...) remotely? Is the iPhone or an iPad of any help? Is there any remote-control app?

The remote app for iPhone will let you control any Mac or PC running iTunes. Remember, though, it controls iTunes, not the whole Mac. There is also a Keynote Remote app that will supposedly let you remote control that app, but I've not tried it, though.